Thank you, Mark. I just built dealii from the source (deal.II-9.3.0-pre). And my little test is passing now. Thanks for the help. -Kaushik
On Wed, Dec 9, 2020 at 4:36 PM Kaushik Das <k.da...@gmail.com> wrote: > Thank you Mark. > I am using the dealii lib that I got from apt-get from > deal.ii-9.2.0-backports. > I used PETSc and the abort was on even 1 cpus. I tried 2, 3, 6 cpus and > all aborted similarly. > > I will get the latest master branch and build that. > > > Thanks, > Kaushik > > On Wed, Dec 9, 2020 at 4:23 PM Marc Fehling <mafehl...@gmail.com> wrote: > >> From your stacktrace I can see you are using PETSc and deal.II 9.2.0 >> which already incorporates the specified patch. Would you try to build the >> actual master branch anyways? >> On Wednesday, December 9, 2020 at 2:11:59 PM UTC-7 Marc Fehling wrote: >> >>> Hi Kaushik, >>> >>> I am unable to reproduce your problem with the code you provided on the >>> latest build of deal.II and Trilinos. >>> >>> - On how many processes did you run your program? >>> - Did you use PETSc or Trilinos? >>> - Could you try to build deal.II on the latest master branch? There >>> is a chance that your issue has been solved upstream. Chances are high >>> that >>> fix #8860 <https://github.com/dealii/dealii/pull/8860> and the >>> changes made to `get_interpolated_dof_values()` will solve your problem. >>> >>> Marc >>> On Wednesday, December 9, 2020 at 7:14:57 AM UTC-7 k.d...@gmail.com >>> wrote: >>> >>>> Hi Marc and Bruno, >>>> I was able to reproduce this abort on an even simpler test. Please see >>>> the attached file. >>>> >>>> Initial grid: >>>> /* >>>> * ----------- >>>> * | 0 | 0 | >>>> * ----------- >>>> * | 1 | 1 | 0 - FEQ, 1 - FE_Nothing >>>> * ----------- >>>> */ >>>> >>>> /* Set refine flags: >>>> * ----------- >>>> * | R | R | FEQ >>>> * ----------- >>>> * | | | FE_Nothing >>>> * ----------- >>>> */ >>>> >>>> Then refine and solution trans. During the >>>> execute_coarsening_and_refinement, it aborts. >>>> >>>> Here is a stack trace: >>>> -------------------------------------------------------- >>>> >>>> An error occurred in line <1167> of file >>>> </build/deal.ii-vFp8uU/deal.ii-9.2.0/include/deal.II/lac/vector.h> in >>>> function >>>> Number& >>>> dealii::Vector<Number>::operator()(dealii::Vector<Number>::size_type) [with >>>> Number = double; dealii::Vector<Number>::size_type = unsigned int] >>>> The violated condition was: >>>> static_cast<typename ::dealii::internal::argument_type<void( >>>> typename std::common_type<decltype(i), decltype(size())>::type)>:: type>(i) >>>> < static_cast<typename ::dealii::internal::argument_type<void( typename >>>> std::common_type<decltype(i), decltype(size())>::type)>:: type>(size()) >>>> Additional information: >>>> Index 0 is not in the half-open range [0,0). In the current case, >>>> this half-open range is in fact empty, suggesting that you are accessing an >>>> element of an empty collection such as a vector that has not been set to >>>> the correct size. >>>> >>>> Stacktrace: >>>> ----------- >>>> #0 /lib/x86_64-linux-gnu/libdeal.ii.g.so.9.2.0: >>>> dealii::Vector<double>::operator()(unsigned int) >>>> #1 /lib/x86_64-linux-gnu/libdeal.ii.g.so.9.2.0: >>>> #2 /lib/x86_64-linux-gnu/libdeal.ii.g.so.9.2.0: >>>> dealii::parallel::distributed::SolutionTransfer<2, >>>> dealii::PETScWrappers::MPI::Vector, dealii::hp::DoFHandler<2, 2> >>>> >::pack_callback(dealii::TriaIterator<dealii::CellAccessor<2, 2> > const&, >>>> dealii::Triangulation<2, 2>::CellStatus) >>>> #3 /lib/x86_64-linux-gnu/libdeal.ii.g.so.9.2.0: >>>> dealii::parallel::distributed::SolutionTransfer<2, >>>> dealii::PETScWrappers::MPI::Vector, dealii::hp::DoFHandler<2, 2> >>>> >::register_data_attach()::{lambda(dealii::TriaIterator<dealii::CellAccessor<2, >>>> 2> > const&, dealii::Triangulation<2, >>>> 2>::CellStatus)#1}::operator()(dealii::TriaIterator<dealii::CellAccessor<2, >>>> 2> > const&, dealii::Triangulation<2, 2>::CellStatus) const >>>> #4 /lib/x86_64-linux-gnu/libdeal.ii.g.so.9.2.0: >>>> std::_Function_handler<std::vector<char, std::allocator<char> > >>>> (dealii::TriaIterator<dealii::CellAccessor<2, 2> > const&, >>>> dealii::Triangulation<2, 2>::CellStatus), >>>> dealii::parallel::distributed::SolutionTransfer<2, >>>> dealii::PETScWrappers::MPI::Vector, dealii::hp::DoFHandler<2, 2> >>>> >::register_data_attach()::{lambda(dealii::TriaIterator<dealii::CellAccessor<2, >>>> 2> > const&, dealii::Triangulation<2, >>>> 2>::CellStatus)#1}>::_M_invoke(std::_Any_data const&, >>>> dealii::TriaIterator<dealii::CellAccessor<2, 2> > const&, >>>> dealii::Triangulation<2, 2>::CellStatus&&) >>>> #5 /lib/x86_64-linux-gnu/libdeal.ii.g.so.9.2.0: >>>> std::function<std::vector<char, std::allocator<char> > >>>> (dealii::TriaIterator<dealii::CellAccessor<2, 2> > const&, >>>> dealii::Triangulation<2, >>>> 2>::CellStatus)>::operator()(dealii::TriaIterator<dealii::CellAccessor<2, >>>> 2> > const&, dealii::Triangulation<2, 2>::CellStatus) const >>>> #6 /lib/x86_64-linux-gnu/libdeal.ii.g.so.9.2.0: >>>> std::_Function_handler<std::vector<char, std::allocator<char> > >>>> (dealii::TriaIterator<dealii::CellAccessor<2, 2> >, >>>> dealii::Triangulation<2, 2>::CellStatus), std::function<std::vector<char, >>>> std::allocator<char> > (dealii::TriaIterator<dealii::CellAccessor<2, 2> > >>>> const&, dealii::Triangulation<2, 2>::CellStatus)> >>>> >::_M_invoke(std::_Any_data const&, >>>> dealii::TriaIterator<dealii::CellAccessor<2, 2> >&&, >>>> dealii::Triangulation<2, 2>::CellStatus&&) >>>> #7 /lib/x86_64-linux-gnu/libdeal.ii.g.so.9.2.0: >>>> std::function<std::vector<char, std::allocator<char> > >>>> (dealii::TriaIterator<dealii::CellAccessor<2, 2> >, >>>> dealii::Triangulation<2, >>>> 2>::CellStatus)>::operator()(dealii::TriaIterator<dealii::CellAccessor<2, >>>> 2> >, dealii::Triangulation<2, 2>::CellStatus) const >>>> #8 /lib/x86_64-linux-gnu/libdeal.ii.g.so.9.2.0: >>>> dealii::parallel::distributed::Triangulation<2, >>>> 2>::DataTransfer::pack_data(std::vector<std::tuple<p4est_quadrant*, >>>> dealii::Triangulation<2, 2>::CellStatus, >>>> dealii::TriaIterator<dealii::CellAccessor<2, 2> > >, >>>> std::allocator<std::tuple<p4est_quadrant*, dealii::Triangulation<2, >>>> 2>::CellStatus, dealii::TriaIterator<dealii::CellAccessor<2, 2> > > > > >>>> const&, std::vector<std::function<std::vector<char, std::allocator<char> > >>>> (dealii::TriaIterator<dealii::CellAccessor<2, 2> >, >>>> dealii::Triangulation<2, 2>::CellStatus)>, >>>> std::allocator<std::function<std::vector<char, std::allocator<char> > >>>> (dealii::TriaIterator<dealii::CellAccessor<2, 2> >, >>>> dealii::Triangulation<2, 2>::CellStatus)> > > const&, >>>> std::vector<std::function<std::vector<char, std::allocator<char> > >>>> (dealii::TriaIterator<dealii::CellAccessor<2, 2> >, >>>> dealii::Triangulation<2, 2>::CellStatus)>, >>>> std::allocator<std::function<std::vector<char, std::allocator<char> > >>>> (dealii::TriaIterator<dealii::CellAccessor<2, 2> >, >>>> dealii::Triangulation<2, 2>::CellStatus)> > > const&) >>>> #9 /lib/x86_64-linux-gnu/libdeal.ii.g.so.9.2.0: >>>> dealii::parallel::distributed::Triangulation<2, >>>> 2>::execute_coarsening_and_refinement() >>>> #10 /home/kdas/FE_NothingTest/build/test_distributed: main >>>> >>>> Thank you very much, >>>> Kaushik >>>> >>>> On Tue, Dec 8, 2020 at 6:25 PM Marc Fehling <mafe...@gmail.com> wrote: >>>> >>>>> Hi Kaushik, >>>>> >>>>> the `p::d::SolutionTransfer` class should be able to deal with >>>>> `FENothing` elements in your example. The tricky cases are when you're >>>>> coarsening a `FENothing` element with others as Bruno already pointed out >>>>> (h-coarsening), or if you change a `FENothing` element to a different >>>>> element in the process (p-adaptation). But with your recent modification, >>>>> you avoid these cases. >>>>> >>>>> I suspect that something else causes the error in your program. Could >>>>> you run a debugger on this and give us the backtrace for the exception? >>>>> This will give us more clues to figure out what goes wrong! >>>>> >>>>> Best, >>>>> Marc >>>>> On Tuesday, December 8, 2020 at 7:13:29 AM UTC-7 k.d...@gmail.com >>>>> wrote: >>>>> >>>>>> Hi Bruno: >>>>>> Thanks for pointing that out. >>>>>> I tried to not refine FE_nothing cells by modifying the refine loop: >>>>>> (The modified test is attached). >>>>>> >>>>>> for (auto &cell : dgq_dof_handler.active_cell_iterators()) >>>>>> if (cell->is_locally_owned() && cell->active_fe_index () != 0) >>>>>> { >>>>>> if (counter > ((dim == 2) ? 4 : 8)) >>>>>> cell->set_coarsen_flag(); >>>>>> else >>>>>> cell->set_refine_flag(); >>>>>> } >>>>>> >>>>>> But this still aborts. >>>>>> Kaushik >>>>>> >>>>>> On Tue, Dec 8, 2020 at 8:36 AM Bruno Turcksin <bruno.t...@gmail.com> >>>>>> wrote: >>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> Are you sure that your test makes sense? You randomly assign FE >>>>>>> indices to cells then you refine and coarsen cells. But what does it >>>>>>> mean >>>>>>> to coarsen 4 cells together when one of them is FE_Nothing? What would >>>>>>> you >>>>>>> expect to happen? >>>>>>> >>>>>>> Best, >>>>>>> >>>>>>> Bruno >>>>>>> >>>>>>> On Monday, December 7, 2020 at 5:54:10 PM UTC-5 k.d...@gmail.com >>>>>>> wrote: >>>>>>> >>>>>>>> Hi all: >>>>>>>> >>>>>>>> I modified the test tests/mpi/solution_transfer_05.cc to add a >>>>>>>> FE_Nohting element to the FECollection. I also modified the other >>>>>>>> elements >>>>>>>> to FE_Q. >>>>>>>> >>>>>>>> When I run the test, it's aborting in solution transfer. >>>>>>>> Is there any limitations in using FE_Nothing with parallel solution >>>>>>>> transfer? >>>>>>>> The modified test is attached. >>>>>>>> Thank you very much. >>>>>>>> Kaushik >>>>>>>> >>>>>>>> ---- >>>>>>>> An error occurred in line <1167> of file >>>>>>>> </build/deal.ii-vFp8uU/deal.ii-9.2.0/include/deal.II/lac/vector.h> in >>>>>>>> function >>>>>>>> Number& >>>>>>>> dealii::Vector<Number>::operator()(dealii::Vector<Number>::size_type) >>>>>>>> [with >>>>>>>> Number = double; dealii::Vector<Number>::size_type = unsigned int] >>>>>>>> The violated condition was: >>>>>>>> static_cast<typename ::dealii::internal::argument_type<void( >>>>>>>> typename std::common_type<decltype(i), decltype(size())>::type)>:: >>>>>>>> type>(i) >>>>>>>> < static_cast<typename ::dealii::internal::argument_type<void( typename >>>>>>>> std::common_type<decltype(i), decltype(size())>::type)>:: type>(size()) >>>>>>>> Additional information: >>>>>>>> Index 0 is not in the half-open range [0,0). In the current >>>>>>>> case, this half-open range is in fact empty, suggesting that you are >>>>>>>> accessing an element of an empty collection such as a vector that has >>>>>>>> not >>>>>>>> been set to the correct size. >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>> The deal.II project is located at http://www.dealii.org/ >>>>>>> For mailing list/forum options, see >>>>>>> https://groups.google.com/d/forum/dealii?hl=en >>>>>>> --- >>>>>>> You received this message because you are subscribed to a topic in >>>>>>> the Google Groups "deal.II User Group" group. >>>>>>> To unsubscribe from this topic, visit >>>>>>> https://groups.google.com/d/topic/dealii/ssEva6C2PU8/unsubscribe. >>>>>>> To unsubscribe from this group and all its topics, send an email to >>>>>>> dealii+un...@googlegroups.com. >>>>>>> To view this discussion on the web visit >>>>>>> https://groups.google.com/d/msgid/dealii/609b0457-ba90-4aa2-a7d1-5b798d5349ebn%40googlegroups.com >>>>>>> <https://groups.google.com/d/msgid/dealii/609b0457-ba90-4aa2-a7d1-5b798d5349ebn%40googlegroups.com?utm_medium=email&utm_source=footer> >>>>>>> . >>>>>>> >>>>>> -- >>>>> The deal.II project is located at http://www.dealii.org/ >>>>> For mailing list/forum options, see >>>>> https://groups.google.com/d/forum/dealii?hl=en >>>>> --- >>>>> You received this message because you are subscribed to a topic in the >>>>> Google Groups "deal.II User Group" group. >>>>> To unsubscribe from this topic, visit >>>>> https://groups.google.com/d/topic/dealii/ssEva6C2PU8/unsubscribe. >>>>> To unsubscribe from this group and all its topics, send an email to >>>>> dealii+un...@googlegroups.com. >>>>> >>>> To view this discussion on the web visit >>>>> https://groups.google.com/d/msgid/dealii/4cd4582b-3168-4b8b-8195-e316b049cfadn%40googlegroups.com >>>>> <https://groups.google.com/d/msgid/dealii/4cd4582b-3168-4b8b-8195-e316b049cfadn%40googlegroups.com?utm_medium=email&utm_source=footer> >>>>> . >>>>> >>>> -- >> The deal.II project is located at http://www.dealii.org/ >> For mailing list/forum options, see >> https://groups.google.com/d/forum/dealii?hl=en >> --- >> You received this message because you are subscribed to a topic in the >> Google Groups "deal.II User Group" group. >> To unsubscribe from this topic, visit >> https://groups.google.com/d/topic/dealii/ssEva6C2PU8/unsubscribe. >> To unsubscribe from this group and all its topics, send an email to >> dealii+unsubscr...@googlegroups.com. >> To view this discussion on the web visit >> https://groups.google.com/d/msgid/dealii/ada069fe-e4cb-455a-bb4b-06a776d4490bn%40googlegroups.com >> <https://groups.google.com/d/msgid/dealii/ada069fe-e4cb-455a-bb4b-06a776d4490bn%40googlegroups.com?utm_medium=email&utm_source=footer> >> . >> > -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/CAC-fs6vYCXifytbVCUAP7%3DAD6eJetTn-NfQ8hEnGJZdDDa0exg%40mail.gmail.com.
